[2026-06-08T07:29:54] Launching Arriba 2.4.0
[2026-06-08T07:29:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:30:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:30:18] Reading chimeric alignments from '1173_K3O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=701853)
[2026-06-08T07:30:52] Marking multi-mapping alignments (marked=495333)
[2026-06-08T07:30:53] Detecting strandedness (reverse)
[2026-06-08T07:30:53] Assigning strands to alignments 
[2026-06-08T07:30:53] Annotating alignments 
[2026-06-08T07:30:56] Filtering duplicates (remaining=574227)
[2026-06-08T07:30:56] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=531955)
[2026-06-08T07:30:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=531955)
[2026-06-08T07:30:56] Filtering viral contigs with expression lower than the top 5 (remaining=531955)
[2026-06-08T07:30:57] Filtering viral contigs with less than 5% coverage (remaining=531955)
[2026-06-08T07:30:57] Estimating fragment length (mate gap mean=-73.5254, mate gap stddev=25.6363, read length mean=109.222)
[2026-06-08T07:30:57] Filtering read-through fragments with a distance <=10000bp (remaining=513667)
[2026-06-08T07:30:57] Filtering inconsistently clipped mates (remaining=502388)
[2026-06-08T07:30:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=491961)
[2026-06-08T07:30:58] Filtering fragments with small insert size (remaining=491822)
[2026-06-08T07:30:58] Filtering alignments with long gaps (remaining=491822)
[2026-06-08T07:30:58] Filtering fragments with both mates in the same gene (remaining=491724)
[2026-06-08T07:30:58] Filtering fusions arising from hairpin structures (remaining=465898)
[2026-06-08T07:30:58] Filtering reads with a mismatch p-value <=0.01 (remaining=199794)
[2026-06-08T07:30:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=73083)
[2026-06-08T07:31:00] Finding fusions and counting supporting reads (total=72717)
[2026-06-08T07:31:02] Merging adjacent fusion breakpoints (remaining=72406)
[2026-06-08T07:31:02] Filtering multi-mapping fusions by alignment score and read support (remaining=41223)
[2026-06-08T07:31:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:31:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=41083)
[2026-06-08T07:31:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=32318)
[2026-06-08T07:31:05] Filtering fusions with <2 supporting reads (remaining=1211)
[2026-06-08T07:31:05] Filtering fusions with an e-value >=0.3 (remaining=456)
[2026-06-08T07:31:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=480)
[2026-06-08T07:31:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=478)
[2026-06-08T07:31:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=478)
[2026-06-08T07:31:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=469)
[2026-06-08T07:31:06] Searching for fusions with spliced split reads (remaining=474)
[2026-06-08T07:31:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=403)
[2026-06-08T07:31:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=400)
[2026-06-08T07:31:07] Searching for fusions with >=4 spliced events (remaining=400)
[2026-06-08T07:31:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=126)
[2026-06-08T07:31:26] Filtering fusions with anchors <=23nt (remaining=93)
[2026-06-08T07:31:26] Filtering end-to-end fusions with low support (remaining=91)
[2026-06-08T07:31:26] Filtering fusions with no coverage around the breakpoints (remaining=91)
[2026-06-08T07:31:26] Indexing gene sequences 
[2026-06-08T07:31:27] Filtering genes with >=30% identity (remaining=63)
[2026-06-08T07:31:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=50)
[2026-06-08T07:31:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=50)
[2026-06-08T07:31:28] Searching for additional isoforms (remaining=53)
[2026-06-08T07:31:28] Assigning confidence scores to events 
[2026-06-08T07:31:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:31:29] Writing fusions to file '1173_K3O_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:31:29] Writing discarded fusions to file '1173_K3O_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:31:33] Freeing resources
[2026-06-08T07:31:36] Done (elapsed time=00:01:42, CPU time=00:01:41, peak memory=4.82gb)